.extractTemplatesFromData
                        Helper function to extract template profiles
                        from user data
DIA_MSstats_Normalized
                        Example pre-processed DIA-MS dataset
MSstatsPrepareDoseResponseFit
                        Prepare data for dose-response fitting with
                        isotonic regression
bootstrapIC50           Bootstrap IC50 Estimates and Confidence
                        Interval (ratio scale)
bootstrapIC50LogScale   Bootstrap IC50 Estimates and Confidence
                        Interval (log scale)
bootstrapIC50Precalculated
                        Bootstrap IC50 with pre-calculated ratios
calculatePeptideWeights
                        Calculate quality-based weights for peptide
                        measurements
calculateTurnoverRatios
                        Calculate turnover ratios from MSstats
                        FeatureLevelData
convertGroupToNumericDose
                        Convert MSstats GROUP labels to numeric dose in
                        nM and extract drug name
doseResponseFit         Drug-protein interaction detection tested by
                        F-test (fitted curve vs average response)
fitIsotonicRegression   Fit Isotonic Regression Model
futureExperimentSimulation
                        Test future experimental design using simulated
                        data with user-defined or default templates
plotHitRateMSstatsResponse
                        Plot hit rates by category
plotIsotonic            Plot Isotonic Regression Model
plot_tpr_power_curve    Visualize detection power across experimental
                        designs
predictIC50             Predict IC50 (dose where response = target) for
                        each protein and drug
predictIC50Parallel     Parallel version of predictIC50 function
run_tpr_simulation      Simulate detection power across experimental
                        design configurations
simulateChemoProteinLevelNonParametric
                        Simulate chemoproteomics data at the protein
                        level - non-parametric approach
visualizeResponseProtein
                        Plot isotonic regression fit with optional IC50
                        for a single protein and drug
